CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds
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Abstract
Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a widely used web server for locating, delineating, and measuring these geometric and topological properties of protein structures. Recent developments in AI-based protein structure prediction such as AlphaFold2 (AF2) have significantly expanded our knowledge on protein structures. Here we present CASTpFold, a continuation of CASTp that provides accurate and comprehensive identifications and quantifications of protein topography. It now provides (i) results on an expanded database of proteins, including the Protein Data Bank (PDB) and non-singleton representative structures of AlphaFold2 structures, covering 183 million AF2 structures; (ii) functional pockets prediction with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AF2-predicted structures and (iii) pocket similarity search function for surface and protein–protein interface pockets. The CASTpFold web server is freely accessible at https://cfold.bme.uic.edu/castpfold/.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Fast and accurate protein structure search with Foldseek
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Fast and accurate protein structure search with Foldseek
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Self-citationStructure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor
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Drugging an undruggable pocket on KRAS
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- Authors
- Ye, B., Tian, W., Wang, B., & Liang, J.
- Affiliations
- University of Illinois Chicago (US)
- Salk Institute for Biological Studies (US)
- The University of Texas Southwestern Medical Center (US)
- Corresponding author
- Liang, Jie
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-05-23
- Volume
- 52
- Issue
- W1
- Pages
- W194-W199
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC11223844
- OpenAlex
- W4398761928
- Cited by
- 180
- References
- 6
- Citations by year
- 2026: 112 · 2025: 59 · 2024: 9
- FWCI
- 24.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc)
- Funders
- NIH (R35GM127084)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein cavities, protein-protein interfaces, AlphaFold2, Gene Ontology, enzyme commission numbers
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